Exploiting graphics processing units for computational biology and bioinformatics.

Interdisciplinary Sciences, Computational Life Sciences
Joshua L PayneJason H Moore

Abstract

Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show...Continue Reading

References

Dec 12, 2007·BMC Bioinformatics·Michael C SchatzAmitabh Varshney
Apr 18, 2008·BMC Bioinformatics·Svetlin A Manavski, Giorgio Valle
Apr 17, 2009·Bioinformatics·Marc A Suchard, Andrew Rambaut
Jul 28, 2009·BMC Research Notes·Nicholas A Sinnott-ArmstrongJason H Moore

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Citations

May 17, 2011·BMC Bioinformatics·Zhiao Shi, Bing Zhang
Jul 16, 2014·BioMed Research International·Paolo CazzanigaGiancarlo Mauri
Aug 10, 2015·The Journal of Chemical Physics·Sergey V Venev, Konstantin B Zeldovich
Jul 13, 2016·Briefings in Bioinformatics·Marco S NobileDaniela Besozzi
Jun 1, 2011·Molecular Informatics·John A Baker, Jonathan D Hirst
Sep 7, 2021·Interdisciplinary Sciences, Computational Life Sciences·Zeyu XiaXiangke Liao

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